Guess what: this wouldn't help for anyone that wanted to put a kepub on a shelf!! [EDITED TO REMOVE A BUNCH OF ARGUMENTS THAT ARE A REHASH OF A PREVIOUSLY BEATEN HORSE BEFORE I POSTED]. The simpler solutions don't always work either.

Anyone that is having issues from a month ago that haven't disappeared at all (assuming you have been syncing) is likely having a deeper issue and may want to try signing out and back into your account on the device (this resets and reloads the database). The server issue seemed to have been fixed and after a sync my duplicates disappeared a while ago (although when I checked just now they are back).